Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species

PLoS One. 2014 Nov 26;9(11):e113657. doi: 10.1371/journal.pone.0113657. eCollection 2014.

Abstract

The genus Echinochloa (Poaceae) includes numerous problematic weeds that cause the reduction of crop yield worldwide. To date, DNA sequence information is still limited in the genus Echinochloa. In this study, we completed the entire chloroplast genomes of two Echinochloa species (Echinochloa oryzicola and Echinochloa crus-galli) based on high-throughput sequencing data from their fresh green leaves. The two Echinochloa chloroplast genomes are 139,891 and 139,800 base pairs in length, respectively, and contain 131 protein-coding genes, 79 indels and 466 substitutions helpful for discrimination of the two species. The divergence between the genus Echinochloa and Panicum occurred about 21.6 million years ago, whereas the divergence between E. oryzicola and E. crus-galli chloroplast genes occurred about 3.3 million years ago. The two reported Echinochloa chloroplast genome sequences contribute to better understanding of the diversification of this genus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA, Plant / genetics
  • Echinochloa / classification
  • Echinochloa / genetics*
  • Evolution, Molecular
  • Genome, Chloroplast*
  • INDEL Mutation
  • Phylogeny
  • Plant Leaves / genetics
  • Sequence Alignment

Substances

  • DNA, Plant

Grants and funding

This work was supported by the National Natural Science Foundation of China (31221004, 31171863), the National Transgenic Research Program (2014ZX001-003), and the Fundamental Research Funds for the Central Universities (2014QNA6023). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Guhe info Corp. provided support in the form of salaries for authors WS and GJ, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.